Having the hashes along with the salt makes it more difficult to brute force the passwords. This is the whole purpose behind salts. Without a salt, I can just create a catalog of all possible combinations of the password, and store the hash of each, and just compared the hashes with the hash in the password file to find passwords in O(1) time.
Yes, root can obtain your real password if he or she tries to. But it shouldn’t be _this_ easy. If root had to install trojans or sniff the traffic to obtain a local user's password (yes I know root does not need a local user password to do anything on the host, but may want to steal it because users in reality do use same passwords for multiple accounts), this would discourage an administrator in a large organization. This also introduces liability. As an administrator, I don't want to be able to see user password in clear text this easily.
If a host were to be compromised, there is some comfort in knowing that strong password hashes stored in /etc/shadow may take a while to be cracked. With a vulnerability like this, if your system is compromised, clear text passwords of users will compromised as well, without any need for the intruder to brute force them.
My opinion is that passwords should never be stored in clear text anywhere, it is just good practice.
